MolSurfer: two-dimensional maps for navigating three-dimensional structures of proteins.
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Amino Acid Sequence↗
Biomedical subjects
D Walther
Publications and source records attributed to D Walther.
Conformational attractors on the Ramachandran map.
Frequency distributions of protein backbone dihedral angles phi and psi have been analyzed systematically for their apparent correlation with various crystallographic parameters, including the resolution at which the protein structures had been determined, the R factor and the free R factor, and the results have been displayed in novel differential Ramachandran maps. With improved sensitivity compared with conventionally derived heuristic Ramachandran maps, such differential maps automatically reveal conformational 'attractors' to which phi/psi distributions converge as the crystallographic resolution improves, as well as conformations tied specifically to low-resolution structures. In particular, backbone angular combinations associated with residues in alpha--helical conformation show a pronounced consolidation with substantially narrowed phi/psi distributions at higher (better) resolution. Convergence to distinct conformational attractors was also observed for all other secondary-structural types and random-coil conformations. Similar resolution-dependent phi/psi evolutions were obtained for different crystallographic refinement packages, documenting the absence of any significant artificial biases in the refinement programs investigated here. A comparison of differential Ramachandran maps derived for the R factor and the free R factor as independent parameters proved the better suitability of the free R factor for structure-quality assessment. The resolution-based differential Ramachandran map is available as a reference for comparison with actual protein structural data under WebMol, a Java-based structure viewing and analysis program (http://www. cmpharm.ucsf.edu/cgi-bin/webmol.pl).
Crystallography↗
Helix-helix packing angle preferences for finite helix axes.
Recently, James Bowie addressed the question of how to normalize correctly the distribution of observed helix-helix packing angles in proteins (Bowie, Nature Struct. Biol. 4:915-917, 1997). A hitherto unrealized yet significant bias toward crossed packing angles was revealed. However, the derived random reference distribution of packing angles requires that helices have to be assumed as infinite in length. Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger.
Models, Molecular↗
Absence of phospholipase A2 activity in genital Mycoplasma hominis.
The clinical relevance of vaginal colonization with Mycoplasma hominis (M hominis) as a cause of prematurity is doubtful. One of the possible pathways which could explain the role of M hominis in the induction of preterm labour is an increased synthesis of prostaglandins by a phospholipase A2 activity. The aim of this study was to prove whether M hominis secrets proteins with a PLA2 activity and to test whether there are strain differences in the enzyme activity between M hominis isolated from women with normal pregnancy and those with preterm labour. Using specific radio-immunoassay we could not measure any PLA2 activity in the supernatant of all investigated M hominis strains. We exclude the mechanism of induction of preterm labour by M hominis via an increased prostaglandin synthesis. Our findings make a relation between vaginal colonization with M hominis and prematurity unlikely.
Female↗
Detection of C-type natriuretic peptide in normal pregnancy.
C-type natriuretic peptide (CNP) is a recently identified member of the family of natriuretic peptides that plays an important role in the regulation of blood pressure, renal function and volume homeostasis. Its effects are mainly hypotensive and natriuretic. CNP is also considered to be an autocrine/paracrine regulator of the endothelium as well as a neuropeptide. Little is known about its role as a circulating substance. There are only few data of CNP plasma levels and changes in disease. Using a highly specific radioimmunoassay we established for the first time CNP plasma levels of normal pregnancies 5.9 +/- 1.5-8.6 +/- 2.1 pg/ml) and a non-pregnant control group (8.1 +/- 1.7 pg/ml). In contrast to atrial natriuretic peptide and brain natriuretic peptide we have not found significant differences of the plasma levels during normal pregnancy and no difference to the non-pregnant control group.
Atrial Natriuretic Factor↗
Identification of a prion protein epitope modulating transmission of bovine spongiform encephalopathy prions to transgenic mice.
There is considerable concern that bovine prions from cattle with bovine spongiform encephalopathy (BSE) may have been passed to humans (Hu), resulting in a new form of Creutzfeldt-Jakob disease (CJD). We report here the transmission of bovine (Bo) prions to transgenic (Tg) mice expressing BoPrP; one Tg line exhibited incubation times of approximately 200 days. Like most cattle with BSE, vacuolation and astrocytic gliosis were confined in the brainstems of these Tg mice. Unexpectedly, mice expressing a chimeric Bo/Mo PrP transgene were resistant to BSE prions whereas mice expressing Hu or Hu/Mo PrP transgenes were susceptible to Hu prions. A comparison of differences in Mo, Bo, and Hu residues within the C terminus of PrP defines an epitope that modulates conversion of PrPC into PrPSc and, as such, controls prion transmission across species. Development of susceptible Tg(BoPrP) mice provides a means of measuring bovine prions that may prove critical in minimizing future human exposure.
Animals↗
Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil.
Cytoskeletal proteins belonging to the spectrin family have an elongated structure composed of repetitive units. The three-dimensional solution structure of the 16th repeat from chicken brain alpha-spectrin (R16) has been determined by NMR spectroscopy and distance geometry-simulated annealing calculations. We used a total of 1035 distance restraints, which included 719 NOE-based values obtained by applying the ambiguous restraints for iterative assignment (ARIA) method. In addition, we performed a direct refinement against 1H-chemical shifts. The final ensemble of 20 structures shows an average RMSD of 1.52 A from the mean for the backbone atoms, excluding loops and N and C termini. R16 is made up of three antiparallel alpha-helices separated by two loops, and folds into a left-handed coiled-coil. The basic unit of spectrin is an antiparallel heterodimer composed of two homologous chains, beta and alpha. These assemble a tetramer via a mechanism that relies on the completion of a single repeat by association of the partial repeats located at the C terminus of the beta-chain (two helices) and at the N terminus of the alpha-chain (one helix). This tetramer is the assemblage able to cross-link actin filaments. Model building by homology of the "tetramerization" repeat from human erythrocyte spectrin illuminates the possible role of point mutations which cause hemolytic anemias.
Amino Acid Sequence↗
Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.
Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.
Algorithms↗
Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms.
After two generations of software systems for the analysis of two-dimensional electrophoresis (2-DE) images, a third generation of such software packages has recently emerged that combines state-of-the-art graphical user interfaces with comprehensive spot data analysis capabilities. A key characteristic common to most of these software packages is that many of their tools are implementations of algorithms that resulted from research areas such as image processing, vision, artificial intelligence or machine learning. This article presents the main algorithms implemented in the Melanie II 2-D PAGE software package. The applications of these algorithms, embodied as the feature of the program, are explained in an accompanying article (R. D. Appel et al.; Electrophoresis 1997, 18, 2724-2734).
Algorithms↗
WebMol--a Java-based PDB viewer.
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Computer Communication Networks↗
Principles of helix-helix packing in proteins: the helical lattice superposition model.
The geometry of helix-helix packing in globular proteins is comprehensively analysed within the model of the superposition of two helix lattices which result from unrolling the helix cylinders onto a plane containing points representing each residue. The requirements for the helix geometry (the radius R, the twist angle omega and the rise per residue delta) under perfect match of the lattices are studied through a consistent mathematical model that allows consideration of all possible associations of all helix types (alpha-, pi- and 3(10)). The corresponding equations have three well-separated solutions for the interhelical packing angle, omega, as a function of the helix geometric parameters allowing optimal packing. The resulting functional relations also show unexpected behaviour. For a typically observed alpha-helix (omega = 99.1 degrees, delta = 1.45 A), the three optimal packing angles are omega a,b,c = -37.1 degrees, -97.4 degrees and +22.0 degrees with a periodicity of 180 degrees and respective helix radii Ra,b,c = 3.0 A, 3.5 A and 4.3 A. However, the resulting radii are very sensitive to variations in the twist angle omega. At omega triple = 96.9 degrees, all three solutions yield identical radii at delta = 1.45 A where Rtriple = 3.46 A. This radius is close to that of a poly(Ala) helix, indicating a great packing flexibility when alanine is involved in the packing core, and omega triple is close to the mean observed twist angle. In contrast, the variety of possible theoretical solutions is limited for the other two helix types. Besides the perfect matches, novel suboptimal "knobs into holes" hydrophobic packing patterns as a function of the helix radius are described. Alternative "knobs onto knobs" and mixed models can be applied in cases where salt bridges, hydrogen bonds, disulphide bonds and tight hydrophobic head-to-head contacts are involved in helix-helix associations. An analysis of the experimentally observed packings in proteins confirmed the conclusions of the theoretical model. Nonetheless, the observed alpha-helix packings showed deviations from the 180 degrees periodicity expected from the model. An investigation of the actual three-dimensional geometry of helix-helix packing revealed an explanation for the observed discrepancies where a decisive role was assigned to the defined orientation of the C alpha-C beta vectors of the side-chains. As predicted form the model, helices with different radii (differently sized side-chains in the packing core) were observed to utilize different packing cells (packing patterns). In agreement with the coincidence between Rtriple and the radius of a poly(Ala) helix, Ala was observed to show greatest propensity to build the packing core. The application of the helix lattice superposition model suggests that the packing of amino acid residues is best described by a "knobs into holes" scheme rather than "ridges into grooves". The various specific packing modes made salient by the model should be useful in protein engineering and design.
Algorithms↗
Brownian dynamics simulation of the lateral distribution of charged membrane components.
Brownian dynamics simulations were performed to study the contribution of electric interactions between charged membrane components to their lateral distribution in a two-dimensional viscous liquid (bilayer lipid membrane). The electrostatic interaction potential was derived from an analytical solution of the linearized Poisson-Boltzmann equation for point charges in an electrolyte solution--membrane--electrolyte solution system. Equilibrium as well as dynamic quantities were investigated. The lateral organization of membrane particles, modelled by mobile cylinders in a homogeneous membrane separating two electrolyte solutions was described by spatial distribution functions, diffusion coefficients and cluster statistics. Disorder, local order and crystal-like arrangements were observed as a function of the particle charge, the closest possible distances between the charges and the particle density. The simulations revealed that the system is very sensitive to the position of the charges with respect to the electrolyte solution-membrane interface. Electrostatic interactions of charges placed directly on the membrane surface were almost negligible, whereas deeper charges demonstrated pronounced interaction. Biologically relevant parameters corresponded at most to local and transient ordering. It was found that lateral electric forces can give rise to a preferred formation of clusters with an even number of constituents provided that the closest possible charge-charge distances are small. It is concluded that lateral electrostatic interactions can account for local particle aggregations, but their impact on the global arrangement and movement of membrane components is limited.
Cell Membrane↗
Intrahelical side chain-side chain contacts: the consequences of restricted rotameric states and implications for helix engineering and design.
Intrahelical side chain-side chain (sc-sc) interactions are assumed to play a crucial role in the formation and stability of alpha-helices, yet it was found that only 37.2% of all helical residues are involved in such close contacts, assuming a specific minimum contact distance. The majority (58.0%) of these were detected between residues with amino acid sequence spacing i, i + 4. The low frequency of intrahelical sc-sc contacts with sequence separations i, i + 1 and i, i + 3, each observed with only about one-third of the i, i + 4 counts, can be directly and generally attributed to the absence of the g- conformation in helices for the dihedral angle chi 1. However, if it was assumed that each side chain may maximally make only one sc-sc contact, as most commonly observed, the percentage of contacting pairs increased relative to the maximum possible pairs for a given sequence spacing by a factor of approximately 4, e.g. from 20.9 to 81.7% for i, i + 4 contacts. Stereochemical reasons are also given for the observation that i, i + 3 contacts are composed largely of ion or polar pairs, while hydrophobic residues dominate the i, i + 4 contacts. No significantly increased density of intrahelical sc-sc contacts with increasing helix length was found. Although there were generally fewer intrahelical contacts between buried helical residues when more contacts were made to the tertiary protein environment, the number of intrahelical contacts did not increase with increasing solvent exposure of the helices. Implications for helix design and the packing of helices are discussed.
Amino Acid Sequence↗
Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding.
Atomic solvation parameters (ASP) are widely used to estimate the solvation contribution to the thermodynamic stability of proteins as well as the free energy of association for protein-ligand complexes. They are also included in several molecular mechanics computer programs. In this work, a total of eight atomic solvation parametric sets has been employed to calculate the solvation contribution to the free energy of folding delta Gs for 17 proteins. A linear correlation between delta Gs and the number of residues in each protein was found for each ASP set. The calculations also revealed a great variety in the absolute value and in the sign of delta Gs values such that certain ASP sets predicted the unfolded state to be more stable than the folded, whereas others yield precisely the opposite. Further, the solvation contribution to the free energy of association of helix pairs and to the disassociation of loops (connection between secondary structural elements in proteins) from the protein tertiary structures were computed for each of the eight ASP sets and discrepancies were evident among them.
Chemical Phenomena↗
[Improved practical roentgenologic diagnosis of pulmonary emphysema using diagnostic lung function methods].
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Diagnosis, Differential↗
Dopamine transporter messenger RNA in Parkinson's disease and control substantia nigra neurons.
Dopamine transporter messenger RNA (mRNA) expression was assessed by in situ hybridization over individual pigmented neurons from the substantia nigra pars compacta in midbrain sections from 7 parkinsonian and 7 age-matched, neurologically normal patients. In the normal control brains, high levels of expression of dopamine transporter mRNA were noted over pigmented neurons in the substantia nigra pars compacta; neurons in the adjacent nucleus paranigralis of the ventral tegmental area displayed less hybridization. Nigra compacta neurons surviving in brains of patients with Parkinson's disease displayed only 57% of the dopamine transporter mRNA hybridization intensity displayed by nigral neurons in normal control brains. The disease-related decrease in the apparent level of dopamine transporter mRNA expression in remaining neurons could reflect neuronal dysfunction. Conceivably, it might also reflect differential vulnerability of those neurons that initially expressed higher levels of this transporter to the insult of parkinsonism.
Aged↗
Synaptic vesicular monoamine transporter expression: distribution and pharmacologic profile.
The human vesicular monoamine transporter (hSVMT) cDNA predicts a protein of 515 amino acids that shares 92% amino acid identity with the rat cDNA. Northern analyses reveal expression of 4.3 kb SVMT mRNAs in rat hypothalamus, midbrain and brainstem, a 3 kb hSVMT mRNA in human brainstem and a 4.8 kb hSVMT mRNA in human hypothalamus. In situ hybridization documents significant SVMT expression in human nigra compacta neurons and in rat hypothalamic neurons whose distribution patterns are identical to those previously reported to display histaminergic markers. COS cell hSVMT expression yielded nanomolar affinities for tetrabenazine and reserpine, micromolar affinities for haloperidol, GBR12909, serotonin, mazindol, nomifensin and d-amphetamine, while dopamine, epinephrine, norepinephrine and histamine each displayed millimolar affinities. These observations extend the pharmacological characterization of hSVMT and studies of its distribution, and indicate likely physiological roles for SVMT in packaging monoamine transmitters including histamine.
Animals↗
Fos family member changes in nucleus caudalis neurons after primary afferent stimulation: enhancement of fos B and c-fos.
In situ hybridization using cDNAs complementary to specific regions of the mRNAs encoding four members of the FOS transcription factor gene family reveals modest levels of hybridization over superficial lamina of the nucleus caudalis of the spinal tract of the trigeminal in sections taken from unstimulated brains. Fos B expression is markedly and rapidly enhanced ipsilateral to electrical stimulation of the trigeminal ganglia. c-fos mRNA also changes; these differences contrast with the lack of significant changes in the low basal levels of expression of fra-1 and fra-2 mRNAs. The prominent change in fos B mRNA is mediated largely by an increase in the number of neurons that express hybridization densities above background after stimulation. This result, taken together with data on stimulation-induced changes in expression of preproenkephalin and other AP-1 transcription factors in wild-type animals and stimulation-induced changes in CAT activity in transgenic mice expressing portions of the proenkephalin promoter, is consistent with a role for the enhanced fos B expression in upregulation of expression of preproenkephalin in these neurons.
Afferent Pathways↗